GetHpltTable

is a user defined path to the folder where the output files
from the HpltFind() function have been saved.

filepath

<code><a rd-options="" href="/link/GetHpltTable?package=MHCtools&version=1.2.1" data-mini-rdoc="MHCtools::GetHpltTable">GetHpltTable</a></code> uses the output files produced by the HpltFind()
function to produce a table with the mean proportion of incongruent sequences
for each nest. If the mean proportion of incongruent sequences is generally
low, but certain nests have many incongruent sequences, biological reasons
may be causing the mismatches, e.g. extra-pair fertilizations or
recombination events.

Ten tools for analysis of major histocompatibility complex (MHC) data in non-
model species. The functions are tailored for amplicon data sets that have been
filtered using the 'dada2' method (for more information visit
<https://benjjneb.github.io/dada2>), but even other data sets can be analyzed,
if the data tables are formatted according to the description in each function.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The HpltFind() function infers putative haplotypes from families in the data
set.
The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of
the haplotype inference.
The PapaDiv() function compares parent pairs in the data set and calculate their
joint MHC diversity, taking into account sequence variants that occur in both
parents.
The CalcPdist() function calculates the p-distances from pairwise comparisons of all
sequences in a data set, and mean p-distances of all pairwise comparisons within each
sample in a data set. The function includes the options to specify which codons to
compare and to calculate amino acid p-distances.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates a fasta file for each sample in the data
set.

Jacob Roved

MHCtools

Analysis of MHC Data in Non-Model Species

GetHpltTable function

<code><a rd-options='' href='GetHpltTable'>GetHpltTable</a></code> uses the output files produced by the HpltFind()
function to produce a table with the mean proportion of incongruent sequences
for each nest. If the mean proportion of incongruent sequences is generally
low, but certain nests have many incongruent sequences, biological reasons
may be causing the mismatches, e.g. extra-pair fertilizations or
recombination events.

GetHpltTable: GetHpltTable() function

Description

Usage

Arguments

Value

See Also

Examples